Chapter 4 │ Page 132 a inity to their NK cell receptor regardless of being subjected to oxidation through plasma treatment. Figure 5: Oxidation does not a ect the binding a inity of the protein complexes. Free energy profiles (i.e. potential of mean force, PMF) of the native and oxidized protein complexes. Errors associated with sampling are shaded accordingly. 3.2. A Closer Look At The Connections Between The Ligands And Receptors The binding of HLA-E to NKG2A/CD94 is dominated by polar interactions mediated by several hydrogen bonds and a number of salt bridges. The crystal structure of HLA-E – NKG2A/CD94 exhibits five salt bridges [41]. Table 4 shows the binding persistence for the salt bridges found in our simulations, i.e. the percentage of time in which the amino acids that form the salt bridge are actually interacting. To consider a salt bridge as “interacting”, we employed a distance threshold of 4.5 Å [58]. In addition, we only included interactions with a binding persistence of over 5%, unless specified otherwise. The salt bridges that are present in the crystal structure are highlighted in Table 4. Notably, two of these salt bridges (Asp163CD94 – Arg75HLAE and Arg137NKG2A – Glu154HLA-E) had a very low binding persistence in our simulations. On the other hand, several salt bridges not reported to be present in the crystal structure are predicted by our simulations to be (transiently) present in solvated state.
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